New Changes
by Marvelite13
Summary: Change can be terrifying. After Puerto Rico, everyone is changed, emotionally or physically, but new enemies are out there, they need to work together to stop them, even if it will tear them apart. Terrible summary. May turn T in later chapters. fitzsimmons, SkyeWard.
1. Chapter 1

**A/N **I do not own any of these characters. This is my first fanfic. Don't forget to R&amp;R, I could use the feedback. Anyway, enjoy.

**Chapter 1**

The ground wouldn't stop shaking, to Skye, it felt like nothing, but she felt pain. Watching Tripp's body fall apart, because of her, has destroyed her. Then she realized, she was the reason he was here, she could of saved him, if she hadn't been so stupid, and hadn't gone into the tunnel, he might still be alive. The shaking stopped, Skye collapsed, she felt her body go limp and darkness over take her eyes.

Coulson and Mack squatted there for what felt like an eternity, In the duck, cover, and hold position. When the shaking stopped, it took awhile for them to regain their balance. "You ok?" Coulson asked Mack. "I think i'm fine, just a bit weary." Mack responded. Coulson glanced over at the walls that were sealed shut. Now some of them were cracking, and one looked like it was about to fall down. "Skye!" they both said together as they slid through one of the cracks. As soon as they entered they saw. Raina, standing over the now-opened Obelisk on the ground, but something wasn't right. There wasn't anything inside of it. "There gone." they heard Raina say. "There GONE!" she screamed louder, making Coulson pull out his I.C.E.R. "Raina, step back from the Obelisk, or I'll shoot." "What was Raina talking about, and what was in the Obelisk?" Raina looked at him, her eyes matching the one's of a tiger. That made Coulson Shoot.

BANG. Raina went down. "Did you?" asked Mack. "Kill her, no." Coulson answered. "Just iced her, we need to get her up. Mack nodded picking her up. "Get back up to May, make sure she's alright, and tell her that it's **really **you, so she knows you aren't being controlled anymore." Coulson orders Mack. He nods, "Copy that." Mack walks away, Raina in his arms. As soon as he was gone, Coulson ran over to the now unconscious Skye. "Skye?' he asked, not expecting a reply. His wish being granted he picked her, up. "Damn, she's much heavier with my scars," he thought. Then he remembered, Trip? Where was he, did he make it out? Then Coulson looked down.

Lying there was Trips T-Shirt, "What the?" Coulson asked himself. Then he remembered. "Trip must of went in after Skye, how could he be so stupid?" he thought to himself. "Oh god, he can't be dead, please don't be dead Trip." his mind continued to wander, until he remembered he still had Skye in his arms. "Ok Skye, lets go." He took a deep breath and started walking. He made to the rope and found May standing there. "What are you doing here." he asked her. "Came to get you, and Skye, did you really think I would let you carry her up there all by yourself?" she asked pointing to the rope. "You head up, I'll take Skye." she continued. Coulson nodded handing her over to May and started to climb. "Are you sure you don't need any help?" Coulson called down as he huffed his way up the rope. "fine" May gritted back. When they got up, they sat down for a breather. "Where's Trip?" May asked. "I didn't see him down there," Coulson started "but I found a shoe and a t-shirt." he finished. "Does Skye know?" May somehow knew that Trip is dead. She was unconscious when I found her, but she could know." Coulson answered. "Lets head to the Quinjet." May stated.

"We have to go get Fitzsimmons," said Bobbi. She, Hunter, Mack, Coulson and Skye, and May had all caught up to each other. "If Tripp is really dead, they could be stranded." Hunter continued. They were making their way back to the Quinjet, knocking off a Hydra soldier here and there. They had to get the Quinjet in the air before the whole place fell apart, the "earthquake" had shaken things up pretty bad.

When they got to the Quinjet, Coulson laid Skye down on the ground. "We should check for any signs of injuries, the earthquake could of done some damage." Bobbi said to Coulson. "I'll wait until we get Fitzsimmons, she doesn't looked that bruised, if theres anything you want to do, get her something to lay her head on," he replied. Bobbi nodded, grabbing something that looked like a backpack. She gently lift Skye's head and then rested it onto the pack. "get strapped in, take off in 2." May confirmed. Everybody strapped in except for Coulson, who took great care to protect Skye from getting hurt in the take off. When they got in the air, he felt a stir come from Skye. Her eyes slowly opened. When she figured out where she was, she freaked out and jumped into a defensive stance.

"Please, don't touch me, I don't want to hurt you, just stay away, please, just stay away." Skye said, looking worriedly around the small jet. "Skye, you're not going to hurt us, we just need to look at your injuries." Coulson calmly. "No, no, no, I killed him, I killed him and it's all my fault. I killed him." Skye started to sputter. "Skye, who did you think you killed?" he asked, "Trip."


	2. Chapter 2

**A/N **alright, here's chapter two. Enjoy.

**Chapter 2**

"Skye, you did not kill Trip, we'll find out who did." Coulson reassured her. "No, he was there, he came to get me but we got locked in." Skye started. "I tried to stop Raina, but it was too late, the Obelisk opened and It all kind of went dark." She added. "Is that it, then you couldn't of killed him Skye your just weary, probably from the earthquake, it was pretty strong, maybe that's what killed him." May said. "No, I remember the earthquake, I remember seeing Trips body fall apart." Skye broke out into a sob, "It was me, I just know it was, the ground was shaking and I saw him, turned to stone." Everyone heard a bang, and saw May there with an I.C.E.R. "What the hell?" Hunter asked. "She was getting ecstatic, she needs sleep." She replies.

Since Coulson was taking watch over Skye, Bobbi headed to the cockpit, where My was already stationed. "I tried making a contact with Fitz and Simmons, seems like the coms are blocked by something." Bobbi told May. "Probably the rubble that fell, they were in the cave, remember?" Bobbi nodded her head. "If you want, Hunter and I could go get them, considering that Coulson is busy with Skye's injury's." Bobbi asked her. "fine, but remember, keep things on work, not personal." Bobbi smiled, "There's nothing personal going on between us." she lied. May didn't believe her for a second, "I'm sure there isn't."

"Remember, it might be hard to get down there, the earthquake could of destroyed the entrances, be careful." Coulson told Bobbi and Hunter. "Roger that sir," Hunter replied. When the plane landed in the field, Bobbi and Hunter exited the quinjet, instead of wearing all their equipment, they had on their jeans and t-shirts. Now looking like normal tourists, they could easily sneak into the tunnel and grab Fitz and Simmons. "How do you suppose we get down there, teleportation?" Hunter joked. "I don't know, we'll find a way in." replied Bobbi.

To their luck, no one was there. It seemed like nothing had happened, the entrance to the temple wasn't blocked by any rocks like they were expecting. "Be careful," Bobbi told Hunter as they entered. "It looks like there is going to be more rocks as we descend." As they continued walking down, it became harder and harder to maintain their balance. Rocks were everywhere. "Fitz, Simmons?" Bobbi called out. "Bobbi?" they heard a familiar British voice call out. "Oh thank god, we didn't think anyone was coming, I tried the comms but they weren't working." Simmons continued. "Don't worry mate, we're coming." Hunter called out. The two pairs slowly made their ways towards each other. "But the equipment," Fitz started to say as soon as he realized that there weren't enough people and space to get the equipment out. "We'll just have to leave it behind, her isn't enough time," Simmons told him. Saddened by the thought of leaving years of work behind, the four slowly made it out of the cave. As soon as they were out Bobbi called Coulson. "I got them out, were heading towards the Quinjet, we'll be there as soon as we can." Bobbi told him. They started making their way through the town trying not too look suspicious. It's kind of hard when two of them are covered in dirt, looking like they just got off of an abandoned island.

"Where's the quinjet?" Simmons asked. "In the field where it was before." Bobbi replied. "Coulson needs you to help Skye." "Why, what happened to her?" asked Simmons. "We don't really know, but Coulson can fill you in as soon as we get there." Said Bobbi. They were almost out of the town when suddenly Hunter spoke out, "um, mates, who are those guys?" he pointed to two men in black suits in sunglasses coming their way. "Run," Bobbi told Fitzsimmons. Bobbi pulled out a gun that was hidden by her shirt. "What about me?" Hunter asked her. "You take one guy I'll take the other." "Got that." Hunter said as they split up. As soon as they went into attack mode, the men caught on, and pulled out their guns. Bobbi ran up to one of them, hitting him in the back of the knees, knocking him towards the ground. Before he could do anything, she knocked him out with a punch to the face. Hunter was having more trouble, him and the guy were in hand-to-hand combat. "Hunter!" Bobbi yelled, "Duck!" Hunter obeyed, ducking in just enough time for Bobbi to shoot. "Thanks," Hunter told her, "no problem." she answered back. "Where's Fitzsimmons?" Hunter asked. "I don't know, probably took off into town, shouldn't be that hard to find them." Bobbi replied. Just as they started to look for them, they heard a screech of tires behind them. Men got out with weapons and surrounded them. "Damn it." Hunter heard Bobbi say under her breath. "Ahh, Agent Morse, Lance Hunter, We've been looking for you." They turned around to see who it was and found someone who shouldn't be standing there, Bakshi.

**A/N **Uh Oh seems like someone escaped, I'll post as soon as I can. don't forget to R&amp;R


	3. Chapter 3

**A/N** here's chapter 3, I hope you enjoy it, thanks for all of the nice reviews.

Chapter 3

"Sir, we found the scientists," said a Hydra agent behind Bakshi. Bobbi and Hunter turned around to find Fitzsimmons, both in handcuffs. "How did you escape, you were in the hospital." Bobbi asked him. "Ahh, I was feeling better so I decided to leave, those agents didn't put up much of a fight, There isn't really much left your 'secret base' now." Bobbi tried to keep a straight face while Bakshi kept talking. "Seems like I didn't need to escape at all, as soon as I was out the door, I was greeted by Hydra, seems like they were planning an attack anyway."

The Hydra unit that attacked them were escorting the four, all in handcuffs, into one of the jeeps. "How did they get you two?" Bobbi asked. "We were running into the town, and we kind of just ran right into two men, who knew who we were, they handcuffed us and brought us two you guys." Simmons replied. "Swell, just swell, how do you suppose we are going to get out of this mess?" Hunter asked. "I don't know, we'll have to find a way out ourselves, since theres know way of reaching Coulson." Bobbi replied. The Hydra agents had taken the coms from them as soon as they figured out they had them. "What does Hydra even want with us?" asked Fitz, the car that they had been in for about 20 minutes was slowly coming to a stop. "I don't know Fitz, but hopefully we'll learn." answered Simmons.

As soon as they were escorted out of the car, they were taken to what looked like a Hydra facility. They were split up, Fitz and Simmons in one room, and Bobbi and Hunter in another. Fitz and Simmons were both tied to chairs, restraining their arms and legs. While Bobbi and Hunter we're just thrown into a room, with no restraints.

"Fitz, how are we going to get our of here?" Simmons asked him. "I don't know, hopefully Coulson will figure out that we're missing, and send help." As soon as he said that, the door open, revealing a man that looked oddly familiar to Fitz. "So your Fitz and Simmons, the scientists I keep hearing about." The man said. Both said nothing but, Fitz recognized the voice. It belonged to Skye's dad.

"What do you want from us?" Simmons asked harshly. Fitz looked at her, she had some steel in her. She definitely has changed sine her undercover mission in Hydra. "I want to know everything about the man who is running your team, how he works, what his tactics are." Cal replied. "And do you think we are going to just give you this information?" Simmons said, mockingly. "oh no, I would be shocked if you just gave me the information, I know how you and your team works, but I believe I have ways of getting it from you." Cal answered pulling out a gun. "Now which one of you wants to answer first?"

—

"May, it's already been two hours, where are they?" Coulson asked her. "They should of been here a long time ago." "I don't know, but I have a bad feeling that something didn't go right." May answered. "Have you tried calling Bobbi?" Coulson asked. "Five times, Coulson, I think I need to go out there, and find them." May said. "You can't leave May, I need someone here," Coulson told her. "We should head back to the bus, Skye can rest there, and you can try to find out what happened to the rest of our team." Coulson continued. "fine," May said, gritting her teeth. May got the quinjet in the air, and headed towards the Bus, which was still cloaked, not too far away. Since they had departed from the bus, which was in the air, it had landed not to far away.

As soon as they touched down, Coulson carried Skye on board, and laid her down in her bunk. Then he made his way towards the use-to-be lab, to stitch up some of his wounds from the fight with Skye's dad. When he finished that, he made his way towards the cockpit, to find May. He wasn't surprised when he found her there. "I found a routing point, Bobbi was wearing a watch, that had a tracker in it, whoever took them, didn't scan for hidden trackers, now we have a location." May told him. "Where?" Coulson asked her. "Some business center here in Puerto Rico, I'm setting a course for there now." she answered him. "Good work." he said back, leaving the cockpit to give May space to set the course.

He was walking in the living room area of the bus, only to find Skye sitting there on one of the couches. "Hey," she said. "Hey yourself, how are you feeling?" asked Coulson. "Better, sorry I kind of freaked out earlier." She apologized. "Skye, you don't need to be sorry, I know I wasn't in that temple with you, but I believe what you said, that can be dramatic, knowing that you might of killed a person, a friend." Coulson told her, sliding into the seat next to her. Skye nodded, still looking a bit weary, "where is everyone?" She asked Coulson. He sighed, "Bobbi and Hunter went to go grab Fitzsimmons, because the earthquake damaged so much, we couldn't reach them on the coms, but they didn't come back, we're tracking them right now through a tracker that was in Bobbi's watch." Coulson said. "Are they dead because of the earthquake, oh god, I don't want more people to die!" Skye stated. "No Skye it wasn't the…" Coulson started to say before Skye cut him off. "It's all my fault." She continued. "Skye, how is it your fault?" Coulson asked her. "Coulson, this might sound crazy, but I think it was me controlling the earthquake."

**A/N I hope you enjoyed this chapter, I'll post as soon as I can. Don't forget to R&amp;R**


	4. Story Update

Sorry guys, I know how much you probably hate when you think a new chapter is going to be posted, and it's just an update. I just wanted to let you guys know that I'm working to get chapter 4 up, I have a lot of stuff to do right now, but I **promise, **that i'll get the new chapter up by Friday. Thanks so much for the awesome comments! they mean so much to me, I love all the helpful feedback. I hope you all had a merry christmas and I hope you have a happy New Year. Again, sorry about the delay. Thanks so much


	5. Chapter 4

**A/N **Here's my New Years gift to you Chapter 4! don't forget to R&amp;R

**Chapter 4**

**Back at the compound**

"Skye will never look at you without wanting to kill you if you hurt one of us." Simmons told Cal. "After she goes through the transformation, she'll care for none of you, you won't matter to her." He told them. "Well, I'm pretty sure Skye will…" "THAT'S NOT HER NAME!" Cal said, cutting off Fitz. "Well what ever her name is, she wouldn't want you killing us, your wrong, maybe you're never meant to be a father!" Simmons screamed back, not caring what would happen to her. That made Cal loose it. Being told he was never meant to be a father, after years and years of trying to reunite with his daughter, pushed him over the edge. He aimed the gun at Simmons,and pulled the trigger.

Bobbi and Hunter heard a scream that was to familiar. "Simmons." they said in unison. "Ok, we need a way out of here." Bobbi said. "Well we're defenseless." Hunter pointed out. "Thank you, captain obvious." Bobbi replied back, a hint of sarcasm in her voice. "We just need a way to pick the lock to get our weapons, or any weapons, and get Fitzsimmons out." Hunter continued. "Good thing they didn't check for bobby pins." Bobbi said, with a smug look on her face, pulling a bobby pin out of her hair. "Great, how long have you had that in your hair?" Hunter said, a little annoyed. "I had to wait to make sure no one was coming in." Bobbi answered back. "I still think we should wait until someone comes in, so we can have the advantage and not to have to worry about getting the door open." Bobbi said. Like it was on Que., the door opened revealing a heavily armed Hydra soldier. Before he could say anything, Bobbi threw a punch at his face, knocking him down, and with a kick, he was out. "Grab a gun, we need to get out of here fast." Bobbi told Hunter.

They both took a gun from the unconscious Hydra soldier, and headed down the hallway, shooting every soldier that came in their way. "Bob, look." Hunter said, tilting his head towards a locked door. "We should start checking any doors, to see if Fitz and Simmons are in one of the rooms." "We need keys." Bobbi pointed out. "Good thing I have them." Hunter said, with a smug look on his face. "Where did you get them?" Bobbi asked. "All the guards have keys, so I took a set from one of the guards we knocked out." He replied. "Ok, start checking."

Before any of the firefight started, Bakshi entered the room and saw what Cal did. "You fool, I needed her, the orders were to bring her to me, not to shoot her." Bakshi angrily said, not caring that Fitz was there. "I had my own plans, just like I have my own plans for you." Cal said, aiming the gun at Bakshi. Bakshi, with no sign of emotion, just stared back at Cal. "Don't you think I don't know, you need me to get to your daughter." Cal looked surprise, how did Bakshi know? Like he was reading his mind, Bakshi continued. "Of course I know, Whitehall called me, telling me to keep a watch on you." "How did he know you escaped?" Cal asked. "News travels quickly, my friend." Bakshi answered. "Then you also that I killed Whitehall, I don't need you to get to my daughter, she'll come to me." Cal said, just as he was cut off by the door opening. "FREEZE!" shouted Bobbi. "Freeze or i'll shoot." she continued. The two men both put there hands up. Bobbi and Hunter both took out handcuffs that they had stolen from guards, and handcuffed Bakshi and Cal. With Hunter watching them, a gun pointed at each man, Bobbi went over to untie Fitz. As soon as she did that, he ran over to Simmons. She had been shot in the thigh. "we, we, need to get her to a hospital." Fitz stuttered. "We don't have enough man power to carry Simmons, take Bakshi and Skye's dad, and fight off any guard that comes our way." Bobbi replied. "Good thing it won't be just the three of you," came a voice behind them. They turned around to find May and Mack.

"Oh thank god." Hunter sighed. "Mack, you take Simmons, Hunter you take Skye's dad and Bakshi, Fitz get behind us and try to stay out of the fire fight." May ordered everyone. They started making their way out of the building, May and Bobbi fighting off every guard that came near them until they got out of the building. "Where's the jet?" Bobbi asked. "Over here." May pointed to a grassy clearing were the cloaked Quinjet was at.

When everyone got situated, May got the jet in the air, and in 10 minutes they were on the Bus. Coulson had heard what had happened to Simmons, so, he kept Skye in her room. He knew she seeing Simmons would make this whole situation worse. And on top of that, he didn't want Skye knowing that her father was on the bus. She already thought she had earthquake powers, why worry her more. He'll tell her soon enough.

"So, the playground is gone." Coulson said to Bobbi, she nodded. "I don't know if the doctors here are trained enough to help Simmons, most of them are still in training." Bobbi told him. "Are there anymore safe houses?" She asked him. "I don't know, and I don't know if I'm going to be able to reach Fury, he's gone of the grid." He replied. "I know it's a risk, but we should take her to a regular hospital, since there are no more S.H.I.E.L.D trauma centers." Bobbi continued. "I think that's the right call, I'll tell May to set a course for the nearest hospital." He said, walking out of the medical pod where Simmons was being held. Poor Fitz, as much as he wanted to be in there, the emotional memories of his and Simmons's time in that medical pod was unbearable. He simply watched from the outside.

"May, I need you to set a course for the nearest hospital, ASAP." Coulson told May over the coms. "Got that." She answered back. "Bobbi and Fitz, your coming with me to the hospital, May, Hunter and Mack, your staying here."Coulson told everyone. They had all gathered in the common room. Everyone was leaving, but Coulson stopped May. "Take care of Skye, she's been very emotional since whatever happened in the Temple, I want you to keep an eye on her, and I want you to be the one who tells her that her father is on the Bus."Coulson said to her. "alright." May replied back.

With permission of General Talbot, they landed at the nearest airfield. Bobbi and Coulson carefully carried Simmons into one of the vans, and placed her on a gurney. Fitz was watching from the sides. As soon as she was in the van, Fitz situated himself right next to her, reaching out to hold her hand. He glanced over at her leg. The scientists who were on the bus, had cleaned up her leg, and bandaged it, but, They still needed a doctors help. The wound was still deep, and she had lost a lot of blood. "Fitz, you alright back there?" Bobbi called out. "Fine." He replied. "Take your next left," she instructed Coulson. Soon they pulled up to a hospital. Bobbi ran in to find doctors to take Simmons from the Van inside. When she was taken in, she was immediately put in an emergency room. No one was allowed in, os they all waited in the waiting room.

**Meanwhile on the Bus**

May knocked softly on Skye's door. "Skye?" she called out. "Can I come in?" "Sure," She barely heard a soft voice call back. She walked in her room to find her on her face, tears stained. "Simmons was hurt, wasn't she." Skye asked. May having no trouble being upfront, answered, "yes,, she was shot in the leg. Coulson, Bobbi, and Fitz took her to a hospital." she answered back. Skye just nodded her head. "Skye, there is something you should no." May continued. "The man who shot her, it, was your father, and he's here on the bus."

**A/N **OH NO! Skye now knows her father is on the bus, what is she going to do? thanks for all the reviews, and I did listen to them. Doing the whole, overtime someone talks do a new line, thing, is not really my writing style. It's really hard for me to do. But I might trying. I hope you enjoyed this chapter!


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